A method of processing a substrate, includes: loading the substrate having a silicon-containing film formed thereon into a processing container; a first process of modifying the silicon-containing film by supplying a processing gas containing a halogen-containing gas and a basic gas to the substrate, in a state in which an internal pressure of the processing container is set to a first pressure, to generate a reaction product; a second process of vaporizing the reaction product by setting the internal pressure of the processing container to a second pressure lower than the first pressure; and alternately repeating the modifying the silicon-containing film and the vaporizing the reaction product, wherein subsequent rounds of the first process following the initial first process in the alternately repeating the modifying the silicon-containing film and the vaporizing the reaction product includes supplying the processing gas to the substrate on which the reaction product remains.